Understanding the mechanism of nonsense mediated mRNA decay in fission yeast

Lead Research Organisation: University of Birmingham
Department Name: Sch of Biosciences

Abstract

A specific aim of our project is to understand the mechanism which links pre-mRNA splicing to translation and nonsense mediated mRNA decay (NMD) (Brogna et al, 2016). It focuses on understanding the cytoplasmic and nuclear function of UPF1, and indirectly that of the other two conserved proteins UPF2 and UPF3 that are also required for NMD in essentially all eukaryotes. Our project requires a combination of classical and advanced molecular biology, genomics and bioinformatics. In particular we use CRISPR-Cas9 (Jacobs et al, 2014) to introduce nonsense mutations and NET-seq and RNA-seq to analyse how this affect transcription and RNA processing.

Publications

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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M01116X/1 01/10/2015 30/09/2023
1644120 Studentship BB/M01116X/1 05/10/2015 30/09/2019 Andrea Colella
 
Description DNA is the genetic material that carries all the information to synthesize proteins, a process also known as gene expression. The conversion between DNA and proteins requires an intermediate molecule, known as mRNA, that represents a copy of the DNA, with some chemical exceptions: the process of making this DNA copy is termed transcription. During transcription several modifications will occur on the newly formed mRNA molecules: splicing for example, is the process that removes sections of the mRNA that are not necessary for the production of the proteins. When splicing occurs the composition of the mRNA is also altered by the deposition of a stable group of proteins called Exon Junction Complex (EJC) factors, that are believed to be involved in a RNA quality control mechanism, which allows to remove defective mRNAs that are deleterious for the organism and can cause diseases.
Contrary to consensus I found that the core component of the EJC, known as eIF4A3, can be deposited on the mRNA independently of splicing, and it affects the expression of the genes where it is bound, suggesting a pivotal function in transcription regulation. I also found that eIF4A3 is localised not only on the DNA, but also in the nucleolus, a region of the cell where some specific RNAs, known as ribosomal RNAs (rRNAs) are produced: here eIF4A3 is mainly involved in the formation of an important type of rRNA, the 18s, which is a core component of the ribosome, the machinery that converts the mRNAs in proteins. Therefore eIF4A3 plays a role not only in transcription, but indirectly it has some roles also in translation.
The project has been carried out in collaboration with Kayoko Tanaka, Principal Investigator at the University of Leicester. This collaboration has allowed to explore and implement several cutting edge technologies, to induce the depletion of the eIF4A3 in a controlled manner. Particularly we have focused on two of these technologies: the Auxin-Inducible degron system, that permits the depletion of a protein of interest in almost 30 minutes, and the promoter shut-off approach, that allows the depletion of eIF4A3 in almost 12 hours.
Exploitation Route My results demonstrate that the core component of the Exon Junction Complex (EJC), eIF4A3, is recruited on mRNA independently of splicing events and it could affects global gene expression. These results should yield further insights into the basic gene expression mechanisms, not only clarifying how eukaryotic genes are expressed and regulated, but also changing the current notions in the field of molecular biology. Because defects in the EJC factors have been correlated to neurodevelopment pathologies and rare human diseases, my results could clarify the etiology behind these conditions and contribute to the development of new therapies and treatments.
Sectors Education,Healthcare,Pharmaceuticals and Medical Biotechnology

 
Description Because defects or deficiencies in the EJC factors have been correlated to neurodevelopment pathologies and rare human diseases, my results could clarify the etiology behind these conditions and contribute to the development of new therapies and treatments. Patients suffering from these diseases, have to face psychological and emotional issues, as depression and anxiety, alterations of physical functions, social avoidance, refusal of social interaction, inability to find a job and support themselves or their family. These issues affect not only the patient but also their family and the community. Investigating further insights into the basic mechanisms of gene expression, could contribute to the development of new gene-based therapeutics approaches that could change the existence of the patients, alleviating suffering and improving the quality of life. Finding a cure for these patients will also reduce the cost of hospitalization, the use of equipment, facilities, medical supplies and hospital services. The development of new drugs could dramatically affect the UK growth outcomes, by creating new private bio-pharmaceutical start-ups and/or university spin-off, whose aim is to research, develop and commercialize the new compounds. University spin-offs could increase collaborations between different sectors, encouraging mobility, cooperation and partnerships among different faculties, students and corporate environments.
Sector Education,Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal,Economic